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Title: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

Journal Article · · The Plant Journal
DOI:https://doi.org/10.1111/tpj.13041· OSTI ID:1438259
 [1];  [1];  [2];  [2];  [3];  [2];  [4];  [2];  [1];  [2];  [5];  [6];  [7];  [1]
  1. Michigan State Univ., East Lansing, MI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Plant Biology
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  4. Univ. of Oklahoma, Norman, OK (United States). Dept. of Microbiology and Plant Biology
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  6. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center. Dept. of Agronomy
  7. Univ. of Wisconsin, Madison, WI (United States). DOE Great Lakes Bioenergy Research Center; USDA-ARS Dairy Forage Research Center, Madison, WI (United States)
+ Show Author Affiliations

Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.

Research Organization:
Univ. of Wisconsin, Madison, WI (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Michigan State Univ., East Lansing, MI (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
FC02-07ER64494; AC02-05CH11231
OSTI ID:
1438259
Alternate ID(s):
OSTI ID: 1616044
Journal Information:
The Plant Journal, Vol. 84, Issue 4; ISSN 0960-7412
Publisher:
Society for Experimental BiologyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 30 works
Citation information provided by
Web of Science

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Cited By (16)

Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing
  • Evans, Joseph; Crisovan, Emily; Barry, Kerrie
  • Dryad Digital Repository-Supplementary information for journal article at DOI: 10.1111/tpj.13041, 10 files https://doi.org/10.5061/dryad.nh8ph.2
dataset December 2015
Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing
  • Evans, Joseph; Crisovan, Emily; Barry, Kerrie
  • Dryad Digital Repository-Supplementary information for journal article at DOI: 10.1111/tpj.13041, 10 files https://doi.org/10.5061/dryad.nh8ph.1
dataset October 2015
Genome-Wide Association Study in Pseudo-F2 Populations of Switchgrass Identifies Genetic Loci Affecting Heading and Anthesis Dates journal September 2018
DNA-Based Assessment of Genetic Diversity in Grassland Plant Species: Challenges, Approaches, and Applications text January 2019
DNA-Based Assessment of Genetic Diversity in Grassland Plant Species: Challenges, Approaches, and Applications journal December 2019
Photosynthesis capacity diversified by leaf structural and physiological regulation between upland and lowland switchgrass in different growth stages journal January 2020
Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing dataset December 2015
Genome size variation in the genus Avena journal March 2016
Marker‐trait association analysis for postharvest needle retention/abscission in balsam fir ( Abies balsamea ) journal May 2019
Genome-Wide Associations with Resistance to Bipolaris Leaf Spot (Bipolaris oryzae (Breda de Haan) Shoemaker) in a Northern Switchgrass Population (Panicum virgatum L.) posted_content August 2019
Quantitative Trait Locus Mapping for Flowering Time in a Lowland × Upland Switchgrass Pseudo-F Population journal January 2018
Genomic prediction accuracy for switchgrass traits related to bioenergy within differentiated populations journal July 2018
Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.) journal June 2018
Crop-associated virus infection in a native perennial grass: reduction in plant fitness and dynamic patterns of virus detection journal January 2017
Gas exchange characteristics and their influencing factors for halophytic plant communities on west coast of Bohai Sea journal February 2020
Extensions of BLUP Models for Genomic Prediction in Heterogeneous Populations: Application in a Diverse Switchgrass Sample journal March 2019

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59 BASIC BIOLOGICAL SCIENCES
09 BIOMASS FUELS
Panicum virgatum
exome capture
switchgrass
polyploid
genomics
PRJNA280418